An official website of the United States government
ABSTRACT Biophysics is an interdisciplinary pursuit requiring researchers with knowledge and skills in several areas. Optical instruments and computers are fundamental tools in biophysics research to collect and analyze data. We developed a 1-semester Optical Engineering Laboratory course to teach image processing, optical engineering, and research skills to undergraduate students majoring in biology and biochemistry. With the use of development systems on students' laptops and in the cloud, students learned image processing with Python and OpenCV. Each student constructed a microprocessor-based lensless holographic microscope, gaining hands-on experience with optical engineering. The class culminated in original, student-designed research projects. All lectures, hands-on labs, and student research projects were performed both in person and remotely, in response to the COVID-19 pandemic.
more »
« less
Open-Ended Inquiry into Zebrafish Nerve Development Using Image Analysis
Open-ended laboratory projects increase student success and retention in the sciences. However, developing organismal-based research projects is a challenge for students with restricted laboratory access, such as those attending courses remotely. Here I describe the use of image analysis of zebrafish neural development for authentic research projects in an introductory biology laboratory course. Zebrafish are a vertebrate model that produce large numbers of externally and rapidly developing embryos. Because zebrafish larvae are transparent, fluorescent reporters marking nervous system structures can be imaged over time and analyzed by undergraduate scientists. In the pilot of this project, remote first-year college students independently developed biological questions based on an image collection comparing zebrafish mutants and wild-type siblings. Students created and mastered techniques to analyze position, organization, and other morphological features of developing neurons and glia in the images to directly test their biological questions. At the end of the course, students communicated their project results in journal article format and oral presentations. Students were able to hone skills in organismal observation and data collection while studying remotely, and they reported excitement at applying lecture-based knowledge to their own independent questions. This module can be adapted by other instructors for both students on- and off-campus to teach principles of neural development, data collection, data analysis, and scientific communication.
more »
« less
- Award ID(s):
- 1941664
- PAR ID:
- 10389418
- Date Published:
- Journal Name:
- Journal of undergraduate neuroscience education
- Volume:
- 20
- Issue:
- 1
- ISSN:
- 1544-2896
- Page Range / eLocation ID:
- A73-A82
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Responding to the need to teach remotely due to COVID-19, we used readily available computational approaches (and developed associated tutorials (https://mdh-cures-community.squarespace.com/virtual-cures-and-ures)) to teach virtual Course-Based Undergraduate Research Experience (CURE) laboratories that fulfil generally accepted main components of CUREs or Undergraduate Research Experiences (UREs): Scientific Background, Hypothesis Development, Proposal, Experiments, Teamwork, Data Analysis, Conclusions, and Presentation1. We then developed and taught remotely, in three phases, protein-centric CURE activities that are adaptable to virtually any protein, emphasizing contributions of noncovalent interactions to structure, binding and catalysis (an ASBMB learning framework2 foundational concept). The courses had five learning goals (unchanged in the virtual format),focused on i) use of primary literature and bioinformatics, ii) the roles of non-covalent interactions, iii) keeping accurate laboratory notebooks, iv) hypothesis development and research proposal writing, and, v) presenting the project and drawing evidence based conclusions The first phase, Developing a Research Proposal, contains three modules, and develops hallmarks of a good student-developed hypothesis using available literature (PubMed3) and preliminary observations obtained using bioinformatics, Module 1: Using Primary Literature and Data Bases (Protein Data Base4, Blast5 and Clustal Omega6), Module 2: Molecular Visualization (PyMol7 and Chimera8), culminating in a research proposal (Module 3). Provided rubrics guide student expectations. In the second phase, Preparing the Proteins, students prepared necessary proteins and mutants using Module 4: Creating and Validating Models, which leads users through creating mutants with PyMol, homology modeling with Phyre29 or Missense10, energy minimization using RefineD11 or ModRefiner12, and structure validation using MolProbity13. In the third phase, Computational Experimental Approaches to Explore the Questions developed from the Hypothesis, students selected appropriate tools to perform their experiments, chosen from computational techniques suitable for a CURE laboratory class taught remotely. Questions, paired with computational approaches were selected from Modules 5: Exploring Titratable Groups in a Protein using H++14, 6: Exploring Small Molecule Ligand Binding (with SwissDock15), 7: Exploring Protein-Protein Interaction (with HawkDock16), 8: Detecting and Exploring Potential Binding Sites on a Protein (with POCASA17 and SwissDock), and 9: Structure-Activity Relationships of Ligand Binding & Drug Design (with SwissDock, Open Eye18 or the Molecular Operating Environment (MOE)19). All involve freely available computational approaches on publicly accessible web-based servers around the world (with the exception of MOE). Original literature/Journal club activities on approaches helped students suggest tie-ins to wet lab experiments they could conduct in the future to complement their computational approaches. This approach allowed us to continue using high impact CURE teaching, without changing our course learning goals. Quantitative data (including replicates) was collected and analyzed during regular class periods. Students developed evidence-based conclusions and related them to their research questions and hypotheses. Projects culminated in a presentation where faculty feedback was facilitated with the Virtual Presentation platform from QUBES20 These computational approaches are readily adaptable for topics accessible for first to senior year classes and individual research projects (UREs). We used them in both partial and full semester CUREs in various institutional settings. We believe this format can benefit faculty and students from a wide variety of teaching institutions under conditions where remote teaching is necessary.more » « less
-
Boury, Nancy Maroushek (Ed.)ABSTRACT Embryonic development is fascinating to follow and highly engaging and, therefore, lends itself for undergraduate students’ first steps in experimental science. We developed the “Trails to Research” inquiry-based course, which exposes students to life science research using zebrafish as model organism. Zebrafish are ideal in the classroom: they are easy to maintain, their embryos develop rapidly, and they are easily manipulated. Further, they lend themselves to teach about embryo development and experimental design. We developed the course for undergraduates at 2-year colleges and, therefore, for students with little or no research experience. In this 5-day intensive course (which is taught during summers as a stand-alone course), students design treatment experiments for zebrafish embryos with known teratogens and with substances they select. The course comprises three modules that overlap over the 5 days: (i) introduction to developmental biology, model organisms, toxicology, and experimental design, (ii) zebrafish embryo experimental setup, and (iii) collecting, analyzing, and presenting data. Student learning was significant in the areas of experimental design, working with model systems, working with zebrafish embryos, using laboratory equipment, and presenting the results of their experiments using effective methods.more » « less
-
Laboratory experimentation is a key component of the development of professional engineers. However, experiments conducted in chemical engineering laboratory classes are commonly more prescriptive than the problems faced by practicing engineers, who have agency to make consequential decisions across the experiment and communication of results. Thus, understanding how experiments in laboratory courses vary in offering students opportunities to make such decisions, and how students navigate higher agency learning experiences is important for preparing graduates ready to direct these practices. In this study, we sought to answer the following research questions: How do students perceive their agency in course-based undergraduate research experiences? What factors are measured by the Consequential Agency in Laboratory Experiments survey? To better understand student perceptions of their agency in relation to laboratory experiments, we first conducted a case study of a course-based research experience (CURE) in a senior-level chemical engineering laboratory course. We then surveyed six upper-division laboratory courses across two universities using an initial version of the Consequential Agency in Laboratory Experiments survey. We used exploratory factor analysis to investigate the validity of the data from the survey for measuring relevant constructs of authenticity, agency in specific domains, responsibility, and opportunity to make decisions. We found that with instructional support, students in the CURE recognized that failure could itself provide opportunities for learning. They valued having the agency to make consequential decisions, even when they also found the experience challenging. We also found strong support for items measuring agency as responsibility, authenticity, agency in the communication domain, agency in the experimental design domain, and opportunity to make decisions. These findings give us insight into the value of higher agency laboratory experiments, and they provide a foundation for developing a more precise survey capable of measuring agency across various laboratory experiment practices. Such a survey will enable future studies that investigate the impacts of increasing agency in just one domain versus in several. In turn, this can aid faculty in developing higher agency learning experiences that are more feasible to implement, compared to CUREs.more » « less
-
null (Ed.)Recently, many faculty have begun to engage students in free and open source software (FOSS) development both for pedagogical advantage and in response to increased student demand. Faculty see FOSS as providing authentic computing artifacts to enrich course content. Students see FOSS projects as a way to contribute to something real and develop their skills while building a portfolio of their work to share with potential employers. Despite these benefits, CS teachers and students have expressed frustration with the challenges of engaging with existing FOSS projects. This BOF will provide a forum for faculty and members of FOSS communities to exchange ideas and methods for engaging students in FOSS, including what did and did not work. The kinds of questions that often arise include whether to let students choose their own projects or select projects for them, and whether to establish mentoring relationships with the project community in advance, or to let students develop these relationships for themselves. Other questions often heard are whether to let students form their own work groups, assign the groups, or if students may work by themselves on a project. Conversely, there are FOSS projects that have questions on how to best engage qualified students. Participant input collected initially will be used to prioritize among the questions above.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- The DOI is not currently available.
